Interpretive Summary: The plant circadian clock orchestrates 24-hour rhythms in a wide-range of important physiological processes. These endogenous rhythms serve to coordinate internal biochemical and regulatory activities with daily and seasonal changes in the environment. As a result, circadian clocks have a direct positive influence on plant fitness. The maize circadian system is not well characterized and its effect on maize physiology is unexplored. Using large-scale microarray analysis of gene expression, this paper establishes transcripts that are subject to circadian regulation. A large number of genes, more than 10% of those studied, have circadian expression. Circadian expression occurs at all times of a 24-hour day, with a preference for dawn and evening. The products of the circadian regulated genes contribute to many important processes, including C4 photosynthesis, carbohydrate metabolism, phytohormone synthesis, and cell wall synthesis. Obvious co-regulation of groups of genes was apparent for enzymes acting within common pathways. This study underscores the fundamental role for circadian regulation in organizing a significant proportion of maize gene expression. A thorough understanding of the maize circadian clock will provide tools to manipulate this system for improvement of maize production and expansion of maize into new environments or for maize adaptation to the changing climate.

Technical Abstract:
The plant circadian clock orchestrates 24-hour rhythms in internal physiological processes to coordinate these activities with daily and seasonal changes in the environment. The circadian clock has a profound impact on many aspects of plant growth and development, including biomass accumulation and flowering time. Despite recent advances in understanding the circadian system of the model plant Arabidopsis thaliana, the contribution of the circadian oscillator to important agronomic traits in Zea mays and other cereals remains poorly defined. To address this deficit, this study investigated the transcriptional landscape of the maize circadian system. RESULTS: Since transcriptional regulation is a fundamental aspect of circadian systems, genes exhibiting circadian expression were identified in the sequenced maize inbred B73. Of the over 13,000 transcripts examined, approximately 10 percent displayed circadian expression patterns. The majority of cycling genes had peak expression at subjective dawn and dusk, similar to other plant circadian systems. The maize circadian clock organized co-regulation of genes participating in fundamental physiological processes, including photosynthesis, carbohydrate metabolism, cell wall biogenesis, and phytohormone biosynthesis pathways. CONCLUSIONS: Circadian regulation of the maize genome was widespread and key genes in several major metabolic pathways had circadian expression waveforms. The maize circadian clock coordinated transcription to be coincident with oncoming day or night, which was consistent with the circadian oscillator acting to prepare the plant for these major recurring environmental changes. These findings highlighted the multiple processes in maize plants under circadian regulation and, as a result, provided insight into the important contribution this regulatory system makes to agronomic traits in maize and potentially other C4 plant species.